| ... | ... |
@@ -225,7 +225,7 @@ seuratObject <- CreateSeuratObject(decontaminated.counts) |
| 225 | 225 |
Conversely, if you have a Seurat object containing raw count matrix and would like to run decontX, simply retrieve the count matrix, convert to SingleCellExperiment, and run on decontX. |
| 226 | 226 |
|
| 227 | 227 |
```{r seuratIntegration2, eval=FALSE}
|
| 228 |
-counts <- seurat@assays$RNA@counts |
|
| 228 |
+counts <- GetAssayData(object = seuratObject, slot = "counts") |
|
| 229 | 229 |
sce <- SingleCellExperiment(list(counts = counts)) |
| 230 | 230 |
sce <- decontX(sce) |
| 231 | 231 |
``` |
